Dear All,
My system:
no mkl
CentOS 7.6 + devtoolset8
cmake-3.25.2 compiled with devtoolset8
openmpi-4.1.8 compiled with devtoolset8
Amber24.tar.bz2 + Amber24.tar.bz2 compiled with devtoolset8
Compilation date: April 7, 2025
Here is a part of my run_cmake file:
[...]
# Assume this is Linux:
export CMAKE_BIN="/opt/cmake-3.25.2/bin/cmake"
$CMAKE_BIN $AMBER_PREFIX/amber24_src \
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber24 \
-DCOMPILER=GNU \
-DMPI=TRUE \
-DOPENMP=TRUE \
-DINSTALL_TESTS=TRUE \
-DDOWNLOAD_MINICONDA=TRUE \
-DCUDA=FALSE \
2>&1 | tee z-cmake_April-7-2024.log
[...]
I get: Miniconda version 3.12 is used.
-- Features:
-- MPI: ON
-- MVAPICH2-GDR for GPU-GPU comm.: OFF
-- OpenMP: ON
-- CUDA: OFF
-- Build Shared Libraries: ON
-- Build GUI Interfaces: ON
-- Build Python Programs: ON
-- -Python Interpreter: Internal Miniconda (version 3.12)
-- Build Perl Programs: ON
-- Build configuration: RELEASE
-- Target Processor: x86_64
-- Build Documentation: ON
-- Sander Variants: normal LES API LES-API MPI
LES-MPI QUICK-MPI
-- Install location: /usr/local/amber24/
-- Installation of Tests: ON
-- Compilers:
-- C: GNU 8.3.1 (/opt/rh/devtoolset-8/root/usr/bin/gcc)
-- CXX: GNU 8.3.1 (/opt/rh/devtoolset-8/root/usr/bin/g++)
-- Fortran: GNU 8.3.1 (/opt/rh/devtoolset-8/root/usr/bin/gfortran)
Summary of AmberTools serial tests:
2975 file comparisons passed
42 file comparisons failed (2 of which can be ignored)
11 tests experienced errors
Test log file saved as
/usr/local/amber24///logs/test_at_serial/2025-04-07_11-56-56.log
Test diffs file saved as
/usr/local/amber24///logs/test_at_serial/2025-04-07_11-56-56.diff
In particular it looks like there are errors related to python3.12.
See below 3 examples (I can send you all the 11 errors if this is useful).
Using a slightly older version such as python3.11 would help ?
thank you
Best Francois
1)
=================================== FAILURES
===================================
______________________________ TestSander.test_GB
______________________________
self = <test_energy.test_sander_energies.TestSander testMethod=test_GB>
.unittest.skipIf(not amberhome, 'skip since there is no AMBERHOME')
def test_GB(self):
# compare to saved test: GB
topfile = os.path.join(amberhome, "test/gb7_trx/prmtop_an")
rstfile = os.path.join(amberhome, "test/gb7_trx/trxox.2.4ns.x")
traj = pt.load(rstfile, topfile)
options = sander.gas_input(7)
options.cut = 9999.0
options.saltcon = 0.2
options.gbsa = 1
edict = pt.esander(traj=traj, mm_options=options, prmtop=topfile)
assert_close(edict['bond'][0], 631.8993, tol=3E-4)
assert_close(edict['angle'][0], 898.2543, tol=3E-4)
assert_close(edict['surf'][0], 33.8338, tol=3E-4)
assert_close(edict['gb'][0], -1943.0838, tol=3E-4)
# dummy test to make sure `esander` can work with list
edict2 = pt.esander(
traj=[
traj,
], mm_options=options, prmtop=topfile, top=traj.top)
> edict3 = pt.esander(
traj=traj(), mm_options=options, prmtop=topfile, top=traj.top)
../../src/pytraj/tests/test_energy/test_sander_energies.py:53:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _ _
../../../lib/python3.12/site-packages/pytraj/utils/decorators.py:11: in inner
return f(*args, **kwd)
../../../lib/python3.12/site-packages/pytraj/utils/get_common_objects.py:314:
in inner
return f(*args, **kwargs)
../../../lib/python3.12/site-packages/pytraj/analysis/energy_analysis.py:186:
in esander
with sander.setup(prmtop_, coords, box, inp, qm_options):
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _ _
self = <SANDER Context; inactive>
prmtop = '/usr/local/amber24//test/gb7_trx/prmtop_an'
coordinates = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ...], box = None
mm_options = <sander.pysander.InputOptions object at 0x2b1533e22970>
qm_options = None
def __init__(self, prmtop, coordinates, box, mm_options, qm_options=None):
# Handle the case where the coordinates are actually a restart file
if isinstance(coordinates, (str, Path)):
# This is a restart file name. Parse it and make sure the
coordinates
# and box
rst = Rst7.open(coordinates)
coordinates = rst.coordinates
if rst.hasbox and (box is None or box is False):
box = rst.box
# Convert from numpy arrays to regular arrays
> coordinates = _np.array(coordinates, copy=False, subok=True)
E ValueError: Unable to avoid copy while creating an array as requested.
E If using `np.array(obj, copy=False)` replace it with
`np.asarray(obj)` to allow a copy when needed (no behavior change in
NumPy 1.x).
E For more details, see
https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword.
../../../lib/python3.12/site-packages/sander/__init__.py:263: ValueError
----------------------------- Captured stdout call
-----------------------------
computed = 631.8992706897363, expected = 631.8993
computed = 898.2542658526359, expected = 898.2543
computed = 33.83379206068037, expected = 33.8338
computed = -1943.083778219314, expected = -1943.0838
________________________ TestSander.test_frame_indices
_________________________
self = <test_energy.test_sander_energies.TestSander
testMethod=test_frame_indices>
def test_frame_indices(self):
traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
frame_indices = [0, 6, 7, 4, 5]
data_without_frame_indices = pt.esander(traj, igb=8)
> data_with_frame_indices = pt.esander(
traj, igb=8, frame_indices=frame_indices)
../../src/pytraj/tests/test_energy/test_sander_energies.py:181:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _ _
../../../lib/python3.12/site-packages/pytraj/utils/decorators.py:11: in inner
return f(*args, **kwd)
../../../lib/python3.12/site-packages/pytraj/utils/get_common_objects.py:314:
in inner
return f(*args, **kwargs)
../../../lib/python3.12/site-packages/pytraj/analysis/energy_analysis.py:186:
in esander
with sander.setup(prmtop_, coords, box, inp, qm_options):
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _ _
self = <SANDER Context; inactive>
prmtop = '/usr/local/amber24/AmberTools/src/pytraj/tests/data/tz2.parm7'
coordinates = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ...], box = None
mm_options = <sander.pysander.InputOptions object at 0x2b15338ed980>
qm_options = None
def __init__(self, prmtop, coordinates, box, mm_options, qm_options=None):
# Handle the case where the coordinates are actually a restart file
if isinstance(coordinates, (str, Path)):
# This is a restart file name. Parse it and make sure the
coordinates
# and box
rst = Rst7.open(coordinates)
coordinates = rst.coordinates
if rst.hasbox and (box is None or box is False):
box = rst.box
# Convert from numpy arrays to regular arrays
> coordinates = _np.array(coordinates, copy=False, subok=True)
E ValueError: Unable to avoid copy while creating an array as requested.
E If using `np.array(obj, copy=False)` replace it with
`np.asarray(obj)` to allow a copy when needed (no behavior change in
NumPy 1.x).
E For more details, see
https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword.
../../../lib/python3.12/site-packages/sander/__init__.py:263: ValueError
=============================== warnings summary
===============================
../../../lib/python3.12/site-packages/parmed/utils/netcdf.py:46
/usr/local/amber24/lib/python3.12/site-packages/parmed/utils/netcdf.py:46:
DeprecationWarning: `np.compat`, which was used during the Python 2 to
3 transition, is deprecated since 1.26.0, and will be removed
from numpy.compat import asbytes, asstr
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
2)
cd cpinutil && ./Run.cpin
Warning: The old format of the CPIN file can only be used for
simulations with temp0=300.0!
You should use the new format for simulations with
temperatures other than 300.0 Kelvins
CPIN generation complete!
Warning: The old format of the CPIN file can only be used for
simulations with temp0=300.0!
You should use the new format for simulations with
temperatures other than 300.0 Kelvins
CPIN generation complete!
Warning: The old format of the CPIN file can only be used for
simulations with temp0=300.0!
You should use the new format for simulations with
temperatures other than 300.0 Kelvins
CPIN generation complete!
Warning: The old format of the CPIN file can only be used for
simulations with temp0=300.0!
You should use the new format for simulations with
temperatures other than 300.0 Kelvins
CPIN generation complete!
Warning: The old format of the CPIN file can only be used for
simulations with temp0=300.0!
You should use the new format for simulations with
temperatures other than 300.0 Kelvins
CPIN generation complete!
Warning: The old format of the CPIN file can only be used for
simulations with temp0=300.0!
You should use the new format for simulations with
temperatures other than 300.0 Kelvins
CPIN generation complete!
Warning: The old format of the CPIN file can only be used for
simulations with temp0=300.0!
You should use the new format for simulations with
temperatures other than 300.0 Kelvins
CPIN generation complete!
Warning: The old format of the CPIN file can only be used for
simulations with temp0=300.0!
You should use the new format for simulations with
temperatures other than 300.0 Kelvins
Traceback (most recent call last):
File "/usr/local/amber24///bin/cpinutil.py", line 332, in <module>
main(opt)
File "/usr/local/amber24///bin/cpinutil.py", line 216, in main
parm = AmberParm(opt.prmtop)
^^^^^^^^^^^^^^^^^^^^^
File
"/usr/local/amber24/lib/python3.12/site-packages/parmed/amber/_amberparm.py",
line 155, in __init__
self.initialize_topology(xyz, box)
File
"/usr/local/amber24/lib/python3.12/site-packages/parmed/amber/_amberparm.py",
line 204, in initialize_topology
self.box = list(box[1:]) + [box[0], box[0], box[0]]
^^^^^^^^
File
"/usr/local/amber24/lib/python3.12/site-packages/parmed/amber/_amberparm.py",
line 2150, in box
box = np.array(box, dtype=np.float64, copy=False,
subok=True).reshape((-1, 6))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: Unable to avoid copy while creating an array as requested.
If using `np.array(obj, copy=False)` replace it with `np.asarray(obj)`
to allow a copy when needed (no behavior change in NumPy 1.x).
For more details, see
https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword.
./Run.cpin: Program error
make[2]: *** [test.cpinutil] Error 1
cd ceinutil && ./Run.cein
CEIN generation complete!
CEIN generation complete!
CEIN generation complete!
CEIN generation complete!
CEIN generation complete!
CEIN generation complete!
Traceback (most recent call last):
File "/usr/local/amber24///bin/ceinutil.py", line 283, in <module>
main(opt)
File "/usr/local/amber24///bin/ceinutil.py", line 192, in main
parm = AmberParm(opt.prmtop)
^^^^^^^^^^^^^^^^^^^^^
File
"/usr/local/amber24/lib/python3.12/site-packages/parmed/amber/_amberparm.py",
line 155, in __init__
self.initialize_topology(xyz, box)
File
"/usr/local/amber24/lib/python3.12/site-packages/parmed/amber/_amberparm.py",
line 204, in initialize_topology
self.box = list(box[1:]) + [box[0], box[0], box[0]]
^^^^^^^^
File
"/usr/local/amber24/lib/python3.12/site-packages/parmed/amber/_amberparm.py",
line 2150, in box
box = np.array(box, dtype=np.float64, copy=False,
subok=True).reshape((-1, 6))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: Unable to avoid copy while creating an array as requested.
If using `np.array(obj, copy=False)` replace it with `np.asarray(obj)`
to allow a copy when needed (no behavior change in NumPy 1.x).
For more details, see
https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword.
./Run.cein: Program error
make[2]: *** [test.ceinutil] Error 1
cd cpeinutil && ./Run.cpein
CPEIN generation complete!
CPEIN generation complete!
CPEIN generation complete!
CPEIN generation complete!
CPEIN generation complete!
Traceback (most recent call last):
File "/usr/local/amber24///bin/cpeinutil.py", line 283, in <module>
main(opt)
File "/usr/local/amber24///bin/cpeinutil.py", line 168, in main
parm = AmberParm(opt.prmtop)
^^^^^^^^^^^^^^^^^^^^^
File
"/usr/local/amber24/lib/python3.12/site-packages/parmed/amber/_amberparm.py",
line 155, in __init__
self.initialize_topology(xyz, box)
File
"/usr/local/amber24/lib/python3.12/site-packages/parmed/amber/_amberparm.py",
line 204, in initialize_topology
self.box = list(box[1:]) + [box[0], box[0], box[0]]
^^^^^^^^
File
"/usr/local/amber24/lib/python3.12/site-packages/parmed/amber/_amberparm.py",
line 2150, in box
box = np.array(box, dtype=np.float64, copy=False,
subok=True).reshape((-1, 6))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: Unable to avoid copy while creating an array as requested.
If using `np.array(obj, copy=False)` replace it with `np.asarray(obj)`
to allow a copy when needed (no behavior change in NumPy 1.x).
For more details, see
https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword.
./Run.cpein: Program error
make[2]: *** [test.cpeinutil] Error 1
cd genremdinputs && ./Run.genremdinputs
diffing output1.1d.dat.save with output1.1d.dat
PASSED
3)
cd 13_Auto_membrane && ./Run.mem
./Run.mem: Program error
make[3]: [MEM_AT] Error 1 (ignored)
make[3]: Leaving directory `/usr/local/amber24/AmberTools/test/mmpbsa_py'
cd bar_pbsa && ./Run.bar_pbsa
Running BAR/PBSA with 1 threads
Skipping complex runs with 1 threads
Namespace(command='strip', strip_input='1C5X_inputs/strip_input.yaml')
{'dest_path': '1C5X', 'complex_paths': ['./1C5X_explicit/t1/complex'],
'ligand_paths': ['./1C5X_explicit/t1/ligands'], 'ligand_mask': ':DRG',
'ion_decharge': True, 'last_half_frames': True, 'stride': 1}
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/complex/t1/0.000
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/complex/t1/0.200
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/complex/t1/0.400
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/complex/t1/0.600
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/complex/t1/0.800
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/complex/t1/1.000
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/ligands/t1/0.000
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/ligands/t1/0.200
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/ligands/t1/0.400
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/ligands/t1/0.600
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/ligands/t1/0.800
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/ligands/t1/1.000
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/concat_complex/0.000
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/concat_complex/0.200
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/concat_complex/0.400
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/concat_complex/0.600
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/concat_complex/0.800
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/concat_complex/1.000
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/concat_ligands/1.000
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/concat_ligands/1.000
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/concat_ligands/1.000
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/concat_ligands/1.000
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/concat_ligands/1.000
mkdir /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/concat_ligands/1.000
Traceback (most recent call last):
File "/usr/local/amber24///bin/bar_pbsa.py", line 736, in <module>
cleaner.run_all()
File "/usr/local/amber24///bin/bar_pbsa.py", line 290, in run_all
self.strip_all_traj()
File "/usr/local/amber24///bin/bar_pbsa.py", line 271, in strip_all_traj
self.strip_single_traj('ligands', lig_path, lamda)
File "/usr/local/amber24///bin/bar_pbsa.py", line 186, in strip_single_traj
atom_idx = self.get_decharged_ion(run_path)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/amber24///bin/bar_pbsa.py", line 99, in get_decharged_ion
parm_in = parmed.amber.AmberParm(str(last_parm))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/usr/local/amber24/lib/python3.12/site-packages/parmed/amber/_amberparm.py",
line 155, in __init__
self.initialize_topology(xyz, box)
File
"/usr/local/amber24/lib/python3.12/site-packages/parmed/amber/_amberparm.py",
line 204, in initialize_topology
self.box = list(box[1:]) + [box[0], box[0], box[0]]
^^^^^^^^
File
"/usr/local/amber24/lib/python3.12/site-packages/parmed/amber/_amberparm.py",
line 2150, in box
box = np.array(box, dtype=np.float64, copy=False,
subok=True).reshape((-1, 6))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: Unable to avoid copy while creating an array as requested.
If using `np.array(obj, copy=False)` replace it with `np.asarray(obj)`
to allow a copy when needed (no behavior change in NumPy 1.x).
For more details, see
https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword.
Namespace(command='prep', prep_input='1C5X_inputs/prep_input.yaml')
{'dest_path': '1C5X', 'ligand_res': 'DRG', 'istrng': 150, 'epsin':
1.0, 'radiscale': 1.0, 'protscale': 1.0}
setup
/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0
setup
/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_complex/e_1.0_r_1.0_p_1.0
Traceback (most recent call last):
File "/usr/local/amber24///bin/bar_pbsa.py", line 741, in <module>
prepper.run_all()
File "/usr/local/amber24///bin/bar_pbsa.py", line 403, in run_all
self.write_sander('ligands')
File "/usr/local/amber24///bin/bar_pbsa.py", line 348, in write_sander
n_frames = self.get_n_frames(ligcom)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/amber24///bin/bar_pbsa.py", line 330, in get_n_frames
trajin = sorted(list(Path(self.dest_path,
f'concat_{ligcom}').rglob('*.nc')))[0]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^
IndexError: list index out of range
Namespace(command='run',
run_input='1C5X_inputs/ligands_run_input.yaml', num_processes=1)
{'dest_path': '1C5X', 'epsin': 1.0, 'radiscale': 1.0, 'protscale':
1.0, 'ligcom': 'ligands', 'del_traj': True}
/usr/local/amber24///bin/sander -i
/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/pb_input.txt -c /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.000/ti.ncrst -p /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.000/ti.parm -O -o /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.000_0.000.out -y /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/0.000/ti001.nc -r /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.000_0.000.ncrst -x /usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.000_0.000_mdcrd -e
/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.000_0.000_mden
[...]
Error opening unit 5: File
"/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/pb_input.txt" is missing or
unreadable
Namespace(command='calc', calc_input='1C5X_inputs/ligands_run_input.yaml')
{'dest_path': '1C5X', 'epsin': 1.0, 'radiscale': 1.0, 'protscale':
1.0, 'ligcom': 'ligands', 'del_traj': True}
parsing
/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.000_0.000.out
parsing
/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.000_0.200.out
parsing
/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.200_0.000.out
parsing
/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.200_0.200.out
parsing
/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.200_0.400.out
parsing
/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.400_0.200.out
parsing
/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.400_0.400.out
parsing
/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.400_0.600.out
parsing
/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.600_0.400.out
parsing
/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.600_0.600.out
parsing
/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.600_0.800.out
parsing
/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.800_0.600.out
parsing
/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.800_0.800.out
parsing
/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/0.800_1.000.out
parsing
/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/1.000_0.800.out
parsing
/usr/local/amber24/AmberTools/test/bar_pbsa/1C5X/param_sweep_ligands/e_1.0_r_1.0_p_1.0/bar_out/1.000_1.000.out
1C5X ligands
bar_total: 0
possible FAILURE: file 1C5X/concat_ligands/0.000/ti001.nc does not exist.
possible FAILURE: file 1C5X/concat_ligands/0.200/ti001.nc does not exist.
possible FAILURE: file 1C5X/concat_ligands/0.400/ti001.nc does not exist.
possible FAILURE: file 1C5X/concat_ligands/0.600/ti001.nc does not exist.
possible FAILURE: file 1C5X/concat_ligands/0.800/ti001.nc does not exist.
possible FAILURE: file 1C5X/concat_ligands/1.000/ti001.nc does not exist.
possible FAILURE: file 1C5X/concat_ligands/0.000/ti.parm does not exist.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 08 2025 - 00:30:02 PDT
